cell_type_name = "CD8T"
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 24.00 25.00 25.00 25.52 26.00 27.00
## [1] 40
## [1] 24 24 24 24 24 24 24 25 25 25 25 25 25 25 25 25 25 25 25 25 25 26 26 26 26
## [26] 26 26 26 26 26 26 27 27 27 27 27 27 27 27 27
## [1] 1021
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "C7orf55"
## [1] "FMC1-LUC7L2" "FMC1"
## [1] "MARS"
## [1] "MARS1" "SLA2"
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "APITD1"
## [1] "CENPS-CORT" "CENPS"
## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"
##
## FALSE TRUE
## 1120 139
##
## FALSE TRUE <NA>
## 71 1049 139
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: ZNRD1 POLR1H
## 2: C2orf43 LDAH
## 3: FAM45A DENND10
## 4: MTERF MTERF1
## 5: NARG2 ICE2
## 6: C6orf203 MTRES1
## 7: HRSP12 RIDA
## 8: FOPNL CEP20
## 9: WARS WARS1
## 10: LINS LINS1
## 11: RRNAD1 METTL25B
## 12: FAM122B PABIR2
## 13: WDYHV1 NTAQ1
## 14: HIST1H2BD H2BC5
## 15: AGPAT6 GPAT4
## 16: C1orf123 CZIB
## 17: KIAA1841 SANBR
## 18: C2orf44 WDCP
## 19: TMEM155 SMIM43
## 20: C7orf55 FMC1-LUC7L2
## 21: C9orf89 CARD19
## 22: C11orf82 DDIAS
## 23: XRCC6BP1 ATP23
## 24: MARS MARS1
## 25: C19orf55 PROSER3
## 26: HIST1H2AE H2AC8
## 27: QARS EPRS1
## 28: APITD1 CENPS-CORT
## 29: CCDC101 SGF29
## 30: PDDC1 GATD1
## 31: EFCAB4A CRACR2B
## 32: EIF2S3L EIF2S3B
## 33: HIST1H2BC H2BC5
## 34: WRB GET1
## 35: TMEM194B NEMP2
## 36: HIST1H4C H4C3
## 37: HIST1H4J H4C11
## 38: ZNF720 KRBOX5
## 39: HIST1H2BH H2BC9
## 40: FAM49A CYRIA
## 41: TTC37 SKIC3
## 42: C1orf85 GLMP
## 43: C9orf114 SPOUT1
## 44: HIST2H2AA4 H2AC19
## 45: HIST2H2BF H2BC18
## 46: C10orf128 TMEM273
## 47: TCTEX1D2 DYNLT2B
## 48: C17orf89 NDUFAF8
## 49: PHBP3 PHB1P3
## 50: SEPT7P7 SEPTIN7P7
## 51: LINC00493 SMIM26
## 52: HIST1H2BN H2BC15
## 53: ATP5J2 ATP5MF
## 54: AKAP2 PALM2AKAP2
## 55: WDR65 CFAP57
## 56: SRP14-AS1 SRP14-DT
## 57: CTC-436P18.1 SMIM15-AS1
## 58: HIST1H3G H3C8
## 59: EFTUD1P1 EFL1P1
## 60: ATP5A1P3 ATP5F1AP3
## 61: CCDC109B MCUB
## 62: C1orf63 RSRP1
## 63: TMEM66 SARAF
## 64: PCNXL2 PCNX2
## 65: ACRC GCNA
## 66: AMICA1 JAML
## 67: PRMT10 PRMT9
## 68: FAM102A EEIG1
## 69: SELM SELENOM
## 70: NBPF16 NBPF15
## 71: RPL9P9 RPL9P8
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]
dim(gene_info)## [1] 1259 3
## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1
## 3: ICA1 ICA1 ICA1
## 4: NDUFAF7 NDUFAF7 NDUFAF7
## 5: ST7 ST7 ST7
## t1
## 1 2
## 1255 2
## sym_in_data sym_limma gene_symbol
## 1: HIST1H2BD H2BC5 H2BC5
## 2: HIST1H2BC H2BC5 H2BC5
## 3: RPL9P8 RPL9P8 RPL9P8
## 4: RPL9P9 RPL9P8 RPL9P8
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]] = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp" "immune"
## reactome go_bp immune
## 1692 7647 5219
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
##
## $immune
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5 162 193 197 199 199 200 200 200 200 1992
## [1] 1259 3
## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=120)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "MCEE" "RPS17" "RPL34" "RPS12"
## [5] "RPS25" "RPL21" "RPL5" "RPS10"
## [9] "SGSM2" "RPS27A" "RPL32" "RPS3A"
## [13] "RPL7" "RPL30" "RPL9" "RPS14"
## [17] "RPL27A" "RPLP2" "RPS27" "RPS23"
## [21] "RPS26" "RPL41" "RPS18" "CTD-2031P19.4"
## [1] 2
## [1] "C1orf112" "TNFRSF9" "WDR13" "ID3"
## [5] "CCRL2" "YIPF2" "FIGNL1" "SLC2A8"
## [9] "SPPL2A" "IRF8" "CCDC51" "SLC39A13"
## [13] "KIR3DL1" "GTSF1" "ZBED2" "YIPF6"
## [17] "TNFRSF18" "KIR2DL4" "GM2A" "KIR2DS4"
## [21] "UBE2D3P2" "RP4-742C19.12" "DBNDD2" "RP11-511H9.4"
## [25] "PHLDB3" "ANKRD37"
## [1] 3
## [1] "LTBP4" "ARHGEF18" "GPN2" "FARP1" "PPP1R32"
## [6] "C7orf55" "TAF10" "KBTBD2" "ATPAF2" "SGMS1"
## [11] "RUFY2" "PCNXL2" "FAM117B" "FBXO32" "EPB41"
## [16] "ATXN7" "ZNF589" "POLR2J3" "YPEL2" "NELL2"
## [21] "TSC22D2" "GPRASP1" "PPP1R10" "RP11-514P8.6" "HCG4P5"
## [1] 4
## [1] "RNF10" "CNOT2" "C3orf14" "AHI1" "APTX" "LINS"
## [7] "PLIN2" "C2orf44" "GLB1" "RRM2" "PCGF5" "CNOT10"
## [13] "EIF4ENIF1" "IFRD1" "DDX3Y" "TNRC6C" "TNRC6B" "UAP1"
## [19] "YPEL5" "CNOT6L" "NR4A2" "BTG2" "PFKFB3" "PLK3"
## [1] 5
## [1] "RABGAP1" "ERGIC2" "GOSR2" "CPD" "NCOA7" "MYB"
## [7] "NARF" "MAP3K6" "LIMD1" "VPS37A" "AGPAT6" "C1orf123"
## [13] "WDR41" "ASB8" "HIST1H4C" "RAB12" "DKK3" "PPP2R5C"
## [19] "CLDND1" "ARRDC2" "LEF1" "SSH2" "C9orf72" "NPAT"
## [25] "RALGAPA1"
## [1] 6
## [1] "ICA1" "GCFC2" "GLT8D1" "MAN2B1" "GBP1" "SCPEP1" "SLC41A2"
## [8] "CLSTN3" "MFSD6" "SLAMF8" "USF1" "ALG8" "MTHFD2L" "GNGT2"
## [15] "ITGAM" "NINJ2" "METRNL" "TMEM107" "PRF1" "BTLA" "NCR3"
## [22] "TRGV3" "TREX1" "KIR3DL2" "KIR2DL3"
## [1] 7
## [1] "ZNRD1" "TIMM9" "POP4" "POLR2I" "GNPTAB" "FAHD2A" "EPAS1"
## [8] "GALE" "UXT" "TMEM241" "TIMM10" "FHOD1" "UCK2" "MPPE1"
## [15] "GALK2" "MED11" "LZTFL1" "POLR2H" "IL15" "CDCA7L" "POP5"
## [22] "TRIM68" "PPARA" "UCKL1" "SELM"
## [1] 8
## [1] "FAM50B" "FCRL6" "CEP57L1" "CALM2P3"
## [5] "RP11-773D16.1" "CTD-2521M24.9" "C1orf63" "ACRC"
## [9] "AMICA1" "CDC42EP3" "ZMAT1" "FILIP1L"
## [13] "RBKS" "CHD2" "LDOC1" "PLGLB1"
## [17] "RP11-91K8.4" "CTD-2328D6.1" "PSMD6-AS2" "MTND4P12"
## [21] "RP11-727F15.9" "QRSL1P3" "RP11-320M16.1" "RP11-335G20.7"
## [25] "RP11-51J9.5"
## [1] 9
## [1] "CDKL1" "PIM2" "TFDP2" "TTLL4"
## [5] "CASP1" "APH1B" "PSEN2" "TMEM134"
## [9] "ANKRD28" "TRAV24" "PSMA6P1" "RP11-122G18.7"
## [13] "RP1-182O16.1" "RNU2-63P" "PHBP3" "RAB1C"
## [17] "AC002331.1" "NDUFA9P1" "RP11-305L7.3" "LINC00426"
## [21] "RPL37P23" "RP11-402J6.3" "SNORD3A" "PLXND1"
## [25] "APBA2" "PLA2G4B"
## [1] 10
## [1] "ZNF419" "PUS7L" "NAALADL1" "RP11-23P13.6"
## [5] "ZNF93" "WDR53" "C2orf76" "ZNF28"
## [9] "RPSAP54" "AC098614.2" "XXbac-B562F10.11" "RP11-2F9.3"
## [13] "RP3-342P20.2" "RP11-567G24.1" "RP11-247I13.6" "AC115617.2"
## [17] "GAPDHP2" "CTD-2301A4.3" "RPL7AP31" "CTB-4E7.1"
## [21] "RP11-307P22.1" "TRAV30" "RP11-209D14.4" "CTB-31O20.3"
## [25] "RP11-686D22.10" "CTB-52I2.4" "TMEM9B-AS1"
## [1] 11
## [1] "SMG6" "MS4A6A" "C2orf43" "L3HYPDH"
## [5] "PGPEP1" "NPL" "IFI44L" "IFI44"
## [9] "TMEM138" "TRANK1" "EDARADD" "TRGV10"
## [13] "TRGV5" "TRBV4-2" "TRAV8-2" "TRGC2"
## [17] "ST13P19" "RPL19P21" "TRGV2" "AC092580.4"
## [21] "RP3-395M20.8" "RP11-33B1.1" "CCL3L3" "CTD-2022H16.3"
## [25] "RP11-345J4.6" "ATP5A1P3"
## [1] 12
## [1] "PLA2G15" "TRPT1" "CMAHP" "ZNF816"
## [5] "RP11-383G10.3" "AC144530.1" "PKMP1" "RP11-32B5.1"
## [9] "RP11-271C24.3" "STARD4-AS1" "MAK" "MAN1C1"
## [13] "ACVR2A" "NBPF14" "C1orf162" "PLAC8"
## [17] "LDLRAP1" "NBPF10" "TMEM150A" "CD248"
## [21] "TRABD2A" "NBPF16" "AC084018.1" "CTD-3092A11.1"
## [25] "RP11-632K20.7" "WHAMMP2"
## [1] 13
## [1] "CHI3L2" "CD200" "PDE6B" "KHDC1"
## [5] "MFSD9" "FUOM" "TNFAIP8L2" "EFCAB4A"
## [9] "ZNF678" "CPT1B" "TRBV9" "TRAV29DV5"
## [13] "RP11-64B16.2" "RP13-383K5.4" "TPI1P2" "RP11-782C8.1"
## [17] "BDH2P1" "SNRPEP4" "LINC00484" "BHLHE40-AS1"
## [21] "RP11-179A18.1" "AC005329.7" "SRP14-AS1" "RP11-81H14.2"
## [25] "KB-1507C5.2" "USP30-AS1" "AP000462.1"
## [1] 14
## [1] "MFAP3" "FAR2" "SH3BP2" "PTPN4" "MICALL1" "CAPN15"
## [7] "CRTAM" "CD86" "MTFR1L" "HRSP12" "DPH6" "FGFBP2"
## [13] "KSR1" "FADS1" "RNF207" "CTLA4" "FRS2" "LRRC28"
## [19] "ZNF80" "PAAF1" "CADM1" "HIST1H4J" "SCML1" "EPHA4"
## [25] "MPP7"
## [1] 15
## [1] "CENPQ" "DHRS12" "RASSF4" "PRR4" "CENPO"
## [6] "ARHGEF1" "PIK3IP1" "RGCC" "EGR1" "PMEPA1"
## [11] "FOSB" "JUND" "SLC38A2" "FAM102A" "JUNB"
## [16] "GOLGA8A" "TTC3" "RGPD6" "MIR4461" "MTND2P28"
## [21] "MTND1P23" "ATP1B3-AS1" "RP11-44N11.1" "SLC7A5P1" "KCNQ1OT1"
## [1] 16
## [1] "WIPI1" "DERL2" "IL4R" "ABHD11" "PTP4A1" "RCOR3" "IFIT2" "TEP1"
## [9] "RSAD2" "FADS2" "BCAS3" "MX1" "AMFR" "FBXO22" "GNG4" "BOLA1"
## [17] "IFIT1" "AGER" "DNASE1" "PVT1" "NEK1" "SIK1" "DHRS3" "SERHL2"
## [1] 17
## [1] "MAD1L1" "CDC27" "CDKN3" "SPTLC2" "ERCC2" "GTF2H3"
## [7] "SMC4" "CACYBP" "CDC20" "STMN1" "CCR2" "CKS2"
## [13] "NPHP4" "CCNB1" "CDK7" "PWP1" "PMAIP1" "CEP78"
## [19] "HIRIP3" "CCNB2" "MYO1E" "ANAPC10" "SESTD1" "C17orf89"
## [25] "TMEM63A"
## [1] 18
## [1] "PTPN18" "NT5C2" "GALK1" "GORASP1"
## [5] "STK25" "CD160" "DHDDS" "NPC2"
## [9] "STYXL1" "KATNBL1" "WARS" "TATDN1"
## [13] "MITD1" "AMDHD2" "CTSB" "GEM"
## [17] "C11orf82" "MEI1" "TBCA" "SMIM19"
## [21] "SPATA13" "PSMG1" "ARHGAP11B" "ANAPC10P1"
## [25] "RP11-638I2.10"
## [1] 19
## [1] "DYRK4" "EGR2" "DTD2" "PIGW"
## [5] "CCDC30" "AC018804.7" "LDHBP2" "MYL5"
## [9] "AC012318.3" "RP11-350G8.3" "GK3P" "SKP1P1"
## [13] "AC093391.2" "RPS27AP2" "CTC-338M12.4" "PTGES3P1"
## [17] "AP000476.1" "AC018462.3" "EEF1A1P10" "HNRNPA1P16"
## [21] "MIR3661" "RP11-282O18.6" "RIMKLB" "RP1-187B23.1"
## [25] "RP13-488H8.1" "LINC00944" "RP11-1000B6.3"
## [1] 20
## [1] "TM7SF3" "GMPR2" "DUS4L" "LOXL3"
## [5] "FANCL" "RNF121" "TBCD" "GEMIN6"
## [9] "CETN3" "NDUFAF6" "PAQR4" "XRCC6BP1"
## [13] "RHEBL1" "NT5DC1" "LRTOMT" "TRAV13-1"
## [17] "NCKIPSD" "RP4-694B14.5" "RPF2P1" "GAPDHP73"
## [21] "RPL13P5" "CTC-436P18.1" "PAICSP4" "RP11-386G11.10"
## [25] "PMF1-BGLAP" "ACTBP9"
## [1] 21
## [1] "TBPL1" "NSMAF" "PMM1" "GZMB" "DDX49"
## [6] "BRD8" "HAVCR1" "MT2A" "NARG2" "PDZD2"
## [11] "GTF2A2" "DRAM2" "GSTM4" "CAPN12" "COA3"
## [16] "CMC1" "ZNF765" "CCL3L1" "TRAV14DV4" "LINC00493"
## [21] "AC104820.2" "RN7SL749P" "TPM3P6" "AC004069.2" "AL358333.1"
## [1] 22
## [1] "OCEL1" "FAM45A" "NME6" "ZNF613"
## [5] "LCORL" "EIF2S3L" "ABHD16B" "RPSAP47"
## [9] "TMEM194B" "METTL6" "RP11-12M9.4" "CD27-AS1"
## [13] "UBXN2B" "ACTBP8" "AC009506.2" "AC010878.3"
## [17] "CCT8P1" "PGAM4" "RP4-800M22.1" "SEPT7P7"
## [21] "PA2G4P4" "PA2G4P2" "RP11-446E9.1" "RP11-473N11.2"
## [25] "RP11-317N8.4" "RP11-493L12.6" "RP11-265N6.3"
## [1] 23
## [1] "FAH" "RRNAD1" "TMSB15B" "KIAA1841"
## [5] "LRRC45" "SNHG11" "AC004840.9" "NAP1L4P1"
## [9] "GEN1" "ZNF257" "TRAV16" "RP1-102E24.1"
## [13] "ATF4P3" "AC090804.1" "ZNF826P" "FAM21FP"
## [17] "RP11-394D2.1" "RNF138P1" "MIR146A" "SLC2A3P4"
## [21] "SF3A3P2" "RP11-416A17.6" "RP11-304L19.5" "RP11-1094M14.7"
## [25] "CTD-2545M3.2" "RP11-705C15.5"
## [1] 24
## [1] "ZNF268" "MDGA1" "MTERF" "CX3CR1"
## [5] "ADCK5" "THAP2" "ZNF683" "SLC9A9"
## [9] "CATSPER2P1" "TRAV19" "TRAV35" "KANSL1-AS1"
## [13] "RPS19P1" "RPL19P12" "RP11-119F19.2" "HNRNPKP2"
## [17] "BTF3P10" "ADH5P4" "AC007041.2" "RPS19P3"
## [21] "GAPDHP60" "RP11-613F22.5" "MIR3615" "LUZP6"
## [25] "RP11-297D21.4" "AC006129.4" "LINC00674"
## [1] 25
## [1] "IL18RAP" "TNFSF10" "PTGER2" "MTHFS"
## [5] "ASNSD1" "XCL1" "XCL2" "C9orf89"
## [9] "ZBTB39" "MT1E" "ENTPD5" "MT1X"
## [13] "ZNF720" "C10orf128" "TRBV20-1" "RSC1A1"
## [17] "NPM1P34" "RP11-262H14.3" "RP11-693N9.2" "ETF1P2"
## [21] "HSPA8P4" "HNRNPA1P55" "TRGV7" "TRAV1-2"
## [25] "EFTUD1P1" "HMGB1P8" "CTD-3214H19.4"
## [1] 26
## [1] "TIPIN" "DUSP12" "DEPDC5" "NSMCE4A"
## [5] "RAD51C" "AKR1A1" "TXNDC17" "TROAP"
## [9] "MMS22L" "SFR1" "PRIMPOL" "UBE2C"
## [13] "SWI5" "ZBTB8OS" "TYMS" "POLE"
## [17] "HIST1H2BC" "HIST2H2AA4" "STK19" "MDP1"
## [21] "RP11-365H23.1" "PIN4P1" "PPIL3" "HIST1H3G"
## [1] 27
## [1] "REXO1" "RP3-324O17.4" "ZNF684" "SLC35A5"
## [5] "TMEM19" "C19orf55" "MTHFD2P7" "PLA2G6"
## [9] "TRAV12-2" "TRDV1" "TRDC" "PDCL3P5"
## [13] "RP5-1053E7.3" "UBA52P6" "LYPLA1P3" "ARPC3P1"
## [17] "RP11-350G13.1" "TCP1P1" "PRDX3P1" "RP11-288E14.2"
## [21] "MAPKAPK5-AS1" "FAM200B" "RNU1-125P" "RP11-382J24.2"
## [25] "AC006483.1" "AC139149.1" "RP4-739H11.4"
## [1] 28
## [1] "MAP3K13" "OAS1" "ZNF85" "IL10"
## [5] "TMEM155" "TECPR1" "RP11-247I13.3" "TSTD1"
## [9] "PTGES3P2" "PATL2" "PET100" "GYG1P3"
## [13] "CNOT7P1" "CDC42P1" "Z97634.3" "ZEB1-AS1"
## [17] "GAPDHP38" "RBBP4P1" "RP11-889L3.4" "AP000620.1"
## [21] "RBBP4P5" "RP11-1012A1.7" "TPMTP1" "AC024592.12"
## [25] "TCEAL3" "AP001468.1"
## [1] 29
## [1] "CD84" "PON2" "KLRB1" "CCL4" "ACTR10" "KLRC1"
## [7] "BORA" "GCHFR" "CXCL13" "PANK4" "FCRL3" "MGAT4B"
## [13] "LGALS9C" "SLC38A9" "WRB" "HLA-DQA1" "CCL4L2" "FAM49A"
## [19] "SH2D1B" "MSH5" "CCL4L1" "KLRC2" "TCTEX1D2" "SAPCD1"
## [25] "MS4A1"
## [1] 30
## [1] "AGA" "GBA2" "RNF13" "USP48" "RABGGTA" "GABPB1" "GSR"
## [8] "ILVBL" "PPFIA1" "PPCDC" "PPOX" "TAMM41" "SEC24D" "FCGR3B"
## [15] "RNF25" "COG5" "ZNF232" "NFU1" "ETFDH" "MZT2A" "TDRD7"
## [22] "FCGR3A" "NR1D2" "WHAMMP3"
## [1] 31
## [1] "MBNL3" "AAAS" "SLC25A14" "LIN7B" "C17orf75" "COQ3"
## [7] "PRMT7" "FOPNL" "TPGS2" "COPS3" "LPP" "CXXC1"
## [13] "NTAN1" "CTDNEP1" "DALRD3" "ZNF511" "C1orf85" "TMSB4X"
## [19] "ATP5J2" "ABHD14A" "MIR142" "GGT7" "OBSCN" "MUC20"
## [25] "MALAT1"
## [1] 32
## [1] "STAU2" "NOP16" "YBX3" "NTHL1" "DOT1L" "DHX58"
## [7] "SLC11A2" "DKC1" "IMP4" "SCRN2" "PELP1" "UTP23"
## [13] "OXSM" "FAM122B" "DBF4B" "ZFP62" "ZNF431" "ZNF770"
## [19] "C9orf114" "ZBTB48" "POTEG" "MIR29B1" "RPS11P5" "AKAP2"
## [1] 33
## [1] "WDR7" "EMG1" "DEF8" "SPON2"
## [5] "HIST2H2BF" "RPS12P26" "GOT2P3" "RP4-728D4.2"
## [9] "CTB-33G10.1" "RASGRF2" "AOAH" "FRMD4A"
## [13] "CXCR5" "AC018720.10" "FAM169A" "HLA-J"
## [17] "RPS26P6" "RPS3AP26" "RP11-572P18.1" "RPL10P3"
## [21] "RPL9P8" "RPL3P4" "RPS3AP6" "HLA-W"
## [25] "RPL9P9" "RPL9P7"
## [1] 34
## [1] "CCL3" "POLD3" "P2RX5" "KIF4A" "ENO3" "NR2C1" "METTL8"
## [8] "DNPEP" "SLC12A4" "SAT1" "SNX14" "PRSS23" "TOMM40L" "TMPRSS3"
## [15] "B2M" "LAIR2" "DNAJC18" "METTL18" "AFMID" "CRYGS" "RGPD5"
## [22] "STK17B" "TMEM66" "EIF1" "CD55"
## [1] 35
## [1] "NHP2P1" "MCM9" "PECR" "NUDT7"
## [5] "CCDC28B" "IFI27" "ZNF749" "EEF1GP1"
## [9] "ZNF649" "ZNF525" "NPM1P32" "NPM1P33"
## [13] "AC009403.2" "RP11-378G13.2" "NPM1P19" "RP11-270C12.3"
## [17] "HNRNPA1P21" "RP11-809F4.2" "TSEN15P1" "RN7SL56P"
## [21] "RP11-552M11.4" "GMPSP1" "RP11-844P9.3" "HMGB1P24"
## [25] "RPPH1" "RP11-265N6.2" "RP13-638C3.4"
## [1] 36
## [1] "EVC" "NFE2L1" "UBXN8" "ZNF544" "RASGRP2"
## [6] "MGAT4A" "TXK" "TCF7" "SLC38A1" "BACH2"
## [11] "HECA" "NR4A3" "CCR7" "PLXDC1" "TIPARP"
## [16] "PRMT10" "DNHD1" "ZBTB20" "TSHZ2" "KLHL25"
## [21] "DENND5A" "SELL" "AC021593.1" "LTB" "RP11-285F7.2"
## [26] "ZNF10" "RP11-747H7.3"
## [1] 37
## [1] "VPS41" "POLA2" "USP28" "WDR3" "PIK3C3" "ULK2"
## [7] "KHSRP" "DHPS" "THOC5" "SNX8" "NUP85" "UROD"
## [13] "C19orf47" "WDR43" "BAP1" "NAA15" "MARS" "ATG13"
## [19] "DUSP28" "PIK3R4" "CHAMP1" "MBD5" "IFRD2" "NAA16"
## [1] 38
## [1] "ORMDL2" "TRAV21" "NAP1L1P3" "RP3-340B19.5"
## [5] "GS1-124K5.2" "EEF1A1P14" "RP11-254B13.4" "RPSAP4"
## [9] "MTRNR2L3" "HSPA8P5" "HNRNPA1P50" "ANP32AP1"
## [13] "AL161784.1" "CPQ" "FOXP1" "RCAN3"
## [17] "BTG1" "TC2N" "GPR183" "SATB1"
## [21] "POU6F1" "ACTBP12" "CHRM3-AS2" "CTD-2017D11.1"
## [25] "RP1-313I6.12" "RP11-434H6.7"
## [1] 39
## [1] "NDUFAF7" "ACADVL" "MTIF2" "MRPS33" "NDUFAF5" "CDK5RAP1"
## [7] "EARS2" "MTFMT" "SARS2" "GTPBP10" "THG1L" "ATPAF1"
## [13] "C6orf203" "MTO1" "MRRF" "GLUD1" "MALSU1" "MRPL55"
## [19] "NDUFS4" "METTL17" "MRPL48" "ZNF782" "MRPL23" "MRPL33"
## [25] "CCDC109B"
## [1] 40
## [1] "BCL3" "GTSE1" "RGS1" "CCDC77" "SMUG1"
## [6] "IFI6" "GLUL" "BRIP1" "IRF4" "PHAX"
## [11] "HOPX" "CXCR6" "PDDC1" "EFCAB7" "RNU2-2P"
## [16] "MIR155HG" "AC011747.4" "DGKA" "SKIL" "RASGEF1B"
## [21] "NPIPB3" "PER1" "NPIPB4" "KLRK1" "NPIPB5"
## [26] "MTATP6P1"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_1"
## [1] "MCEE" "RPS17" "RPL34" "RPS12"
## [5] "RPS25" "RPL21" "RPL5" "RPS10"
## [9] "SGSM2" "RPS27A" "RPL32" "RPS3A"
## [13] "RPL7" "RPL30" "RPL9" "RPS14"
## [17] "RPL27A" "RPLP2" "RPS27" "RPS23"
## [21] "RPS26" "RPL41" "RPS18" "CTD-2031P19.4"
## $reactome
## category
## 21 activation of the mrna upon binding of the cap binding complex and eifs and subsequent binding to 43s
## 117 cellular response to starvation
## 255 eukaryotic translation elongation
## 256 eukaryotic translation initiation
## 387 influenza infection
## 471 metabolism of amino acids and derivatives
## 547 nonsense mediated decay nmd
## 691 regulation of expression of slits and robos
## 734 response of eif2ak4 gcn2 to amino acid deficiency
## 783 rrna processing
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat FDR
## 21 0 1 11 15 0
## 117 0 1 21 33 0
## 255 0 1 21 31 0
## 256 0 1 21 30 0
## 387 0 1 21 37 0
## 471 0 1 21 42 0
## 547 0 1 21 31 0
## 691 0 1 21 31 0
## 734 0 1 21 30 0
## 783 0 1 21 40 0
##
## $go_bp
## category over_represented_pvalue
## 515 cytoplasmic translation 0.000000e+00
## 3691 ribosomal small subunit biogenesis 1.519549e-07
## 3693 ribosome biogenesis 3.069868e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 515 1 21 33 0.0000000000
## 3691 1 7 16 0.0003105198
## 3693 1 9 35 0.0004182183
##
## $immune
## category
## 54 gaucher pbmc yf vax stamaril unknown age 7dy dn
## 1944 gse22886 naive bcell vs neutrophil up
## 1974 gse22886 naive tcell vs dc up
## 2104 gse2405 0h vs 24h a phagocytophilum stim neutrophil up
## 2109 gse2405 0h vs 9h a phagocytophilum stim neutrophil dn
## 3108 gse34205 healthy vs flu inf infant pbmc up
## 4014 gse41978 id2 ko vs id2 ko and bim ko klrg1 low effector cd8 tcell dn
## 4016 gse41978 klrg1 high vs low effector cd8 tcell dn
## 1725 gse21670 untreated vs tgfb il6 treated cd4 tcell dn
## 1628 gse2124 ctrl vs lymphotoxin beta treated mln up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 54 0.000000e+00 1 12 32
## 1944 0.000000e+00 1 12 25
## 1974 0.000000e+00 1 12 33
## 2104 0.000000e+00 1 16 40
## 2109 0.000000e+00 1 15 37
## 3108 0.000000e+00 1 11 25
## 4014 0.000000e+00 1 11 32
## 4016 0.000000e+00 1 12 30
## 1725 5.565068e-12 1 9 17
## 1628 3.572682e-11 1 9 19
## FDR
## 54 0.00000e+00
## 1944 0.00000e+00
## 1974 0.00000e+00
## 2104 0.00000e+00
## 2109 0.00000e+00
## 3108 0.00000e+00
## 4014 0.00000e+00
## 4016 0.00000e+00
## 1725 3.15292e-09
## 1628 1.82171e-08
##
## [1] "set_4"
## [1] "RNF10" "CNOT2" "C3orf14" "AHI1" "APTX" "LINS"
## [7] "PLIN2" "C2orf44" "GLB1" "RRM2" "PCGF5" "CNOT10"
## [13] "EIF4ENIF1" "IFRD1" "DDX3Y" "TNRC6C" "TNRC6B" "UAP1"
## [19] "YPEL5" "CNOT6L" "NR4A2" "BTG2" "PFKFB3" "PLK3"
## $reactome
## category
## 952 tp53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
## 954 tp53 regulates transcription of cell cycle genes
## 981 transcriptional regulation by tp53
## 172 deadenylation of mrna
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 952 5.539692e-08 1.0000000 5 6
## 954 4.270671e-07 1.0000000 5 8
## 981 2.121919e-05 0.9999986 7 35
## 172 9.227516e-05 0.9999994 3 4
## FDR
## 952 5.661566e-05
## 954 2.182313e-04
## 981 7.228670e-03
## 172 2.357630e-02
##
## $go_bp
## category
## 1917 nuclear transcribed mrna poly a tail shortening
## 1913 nuclear transcribed mrna catabolic process deadenylation dependent decay
## 3702 rna destabilization
## 2380 positive regulation of mrna metabolic process
## 1912 nuclear transcribed mrna catabolic process
## 3201 regulation of mrna catabolic process
## 3202 regulation of mrna metabolic process
## 2179 positive regulation of cellular catabolic process
## 1372 mrna catabolic process
## 3257 regulation of nuclear transcribed mrna poly a tail shortening
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1917 3.257384e-11 1.0000000 7 8
## 1913 5.964863e-10 1.0000000 7 10
## 3702 1.204871e-08 1.0000000 7 14
## 2380 4.382508e-08 1.0000000 7 16
## 1912 4.542493e-08 1.0000000 7 15
## 3201 8.928398e-08 1.0000000 7 17
## 3202 4.629271e-07 1.0000000 7 21
## 2179 1.890462e-06 0.9999999 8 33
## 1372 2.026659e-06 0.9999999 7 24
## 3257 2.845476e-06 1.0000000 4 5
## FDR
## 1917 1.331293e-07
## 1913 1.218920e-06
## 3702 1.641435e-05
## 2380 3.713034e-05
## 1912 3.713034e-05
## 3201 6.081727e-05
## 3202 2.702833e-04
## 2179 9.203284e-04
## 1372 9.203284e-04
## 3257 1.162946e-03
##
## [1] "set_9"
## [1] "CDKL1" "PIM2" "TFDP2" "TTLL4"
## [5] "CASP1" "APH1B" "PSEN2" "TMEM134"
## [9] "ANKRD28" "TRAV24" "PSMA6P1" "RP11-122G18.7"
## [13] "RP1-182O16.1" "RNU2-63P" "PHBP3" "RAB1C"
## [17] "AC002331.1" "NDUFA9P1" "RP11-305L7.3" "LINC00426"
## [21] "RPL37P23" "RP11-402J6.3" "SNORD3A" "PLXND1"
## [25] "APBA2" "PLA2G4B"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 858 signaling by notch3 2.616135e-05 0.9999999
## numDEInCat numInCat FDR
## 858 3 5 0.02673689
##
## [1] "set_15"
## [1] "CENPQ" "DHRS12" "RASSF4" "PRR4" "CENPO"
## [6] "ARHGEF1" "PIK3IP1" "RGCC" "EGR1" "PMEPA1"
## [11] "FOSB" "JUND" "SLC38A2" "FAM102A" "JUNB"
## [16] "GOLGA8A" "TTC3" "RGPD6" "MIR4461" "MTND2P28"
## [21] "MTND1P23" "ATP1B3-AS1" "RP11-44N11.1" "SLC7A5P1" "KCNQ1OT1"
## $reactome
## category
## 544 ngf stimulated transcription
## 564 nuclear events kinase and transcription factor activation
## 862 signaling by ntrks
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 544 8.510968e-06 0.9999999 4 7
## 564 1.210001e-05 0.9999999 4 8
## 862 3.174730e-05 0.9999994 4 10
## FDR
## 544 0.006183104
## 564 0.006183104
## 862 0.010815248
##
## [1] "set_17"
## [1] "MAD1L1" "CDC27" "CDKN3" "SPTLC2" "ERCC2" "GTF2H3"
## [7] "SMC4" "CACYBP" "CDC20" "STMN1" "CCR2" "CKS2"
## [13] "NPHP4" "CCNB1" "CDK7" "PWP1" "PMAIP1" "CEP78"
## [19] "HIRIP3" "CCNB2" "MYO1E" "ANAPC10" "SESTD1" "C17orf89"
## [25] "TMEM63A"
## $reactome
## category
## 456 m phase
## 50 apc c cdc20 mediated degradation of cyclin b
## 138 condensation of prometaphase chromosomes
## 500 mitotic metaphase and anaphase
## 501 mitotic prometaphase
## 390 inhibition of the proteolytic activity of apc c required for the onset of anaphase by mitotic spindle checkpoint compone
## 52 apc c mediated degradation of cell cycle proteins
## 283 formation of rna pol ii elongation complex
## 286 formation of the early elongation complex
## 370 hiv transcription elongation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 456 7.030593e-06 0.9999995 8 43
## 50 1.690017e-05 0.9999998 4 7
## 138 2.101969e-05 1.0000000 3 3
## 500 2.392556e-05 0.9999988 6 24
## 501 3.095286e-05 0.9999983 6 25
## 390 8.254878e-05 0.9999995 3 4
## 52 9.599288e-05 0.9999973 4 10
## 283 2.026152e-04 0.9999975 3 5
## 286 2.026152e-04 0.9999975 3 5
## 370 2.026152e-04 0.9999975 3 5
## FDR
## 456 0.006112982
## 50 0.006112982
## 138 0.006112982
## 500 0.006112982
## 501 0.006326766
## 390 0.012942095
## 52 0.012942095
## 283 0.012942095
## 286 0.012942095
## 370 0.012942095
##
## $go_bp
## category over_represented_pvalue
## 1318 mitotic cell cycle phase transition 6.079680e-07
## 1221 meiotic cell cycle 8.499976e-06
## 2926 regulation of chromosome segregation 2.116535e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1318 1.0000000 9 42 0.002484765
## 1221 0.9999996 6 20 0.017369700
## 2926 0.9999993 5 14 0.028834257
##
## $immune
## category
## 3590 gse39556 cd8a dc vs nk cell mouse 3h post polyic inj up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3590 2.650089e-06 0.9999999 7 28
## FDR
## 3590 0.0135128
##
## [1] "set_26"
## [1] "TIPIN" "DUSP12" "DEPDC5" "NSMCE4A"
## [5] "RAD51C" "AKR1A1" "TXNDC17" "TROAP"
## [9] "MMS22L" "SFR1" "PRIMPOL" "UBE2C"
## [13] "SWI5" "ZBTB8OS" "TYMS" "POLE"
## [17] "HIST1H2BC" "HIST2H2AA4" "STK19" "MDP1"
## [21] "RP11-365H23.1" "PIN4P1" "PPIL3" "HIST1H3G"
## $reactome
## category over_represented_pvalue
## 212 dna replication pre initiation 2.649729e-05
## 211 dna replication 5.670078e-05
## 468 meiotic recombination 1.045790e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 212 0.9999991 5 19 0.02708024
## 211 0.9999976 5 22 0.02897410
## 468 0.9999969 4 13 0.03562659
##
## [1] "set_36"
## [1] "EVC" "NFE2L1" "UBXN8" "ZNF544" "RASGRP2"
## [6] "MGAT4A" "TXK" "TCF7" "SLC38A1" "BACH2"
## [11] "HECA" "NR4A3" "CCR7" "PLXDC1" "TIPARP"
## [16] "PRMT10" "DNHD1" "ZBTB20" "TSHZ2" "KLHL25"
## [21] "DENND5A" "SELL" "AC021593.1" "LTB" "RP11-285F7.2"
## [26] "ZNF10" "RP11-747H7.3"
## $immune
## category
## 1268 gse17974 ctrl vs act il4 and anti il12 24h cd4 tcell up
## 56 goldrath eff vs memory cd8 tcell dn
## 136 gse11057 eff mem vs cent mem cd4 tcell dn
## 2958 gse32255 wt unstim vs jmjd2d knockdown 4h lps stim dc up
## 3608 gse3982 bcell vs cent memory cd4 tcell dn
## 2462 gse27241 wt vs rorgt ko th17 polarized cd4 tcell treated with digoxin dn
## 4597 gse7219 unstim vs lps and anti cd40 stim dc up
## 4599 gse7219 unstim vs lps and anti cd40 stim nik nfkb2 ko dc up
## 5060 scherer pbmc apsv wetvax age 18 32yo 5 to 7dy dn
## 425 gse13547 ctrl vs anti igm stim zfx ko bcell 12h dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1268 3.933068e-06 0.9999998 6 20
## 56 4.934628e-06 0.9999998 6 23
## 136 7.856450e-06 0.9999997 6 20
## 2958 1.125513e-05 0.9999995 6 22
## 3608 1.420646e-05 0.9999995 5 15
## 2462 2.907447e-05 0.9999989 5 16
## 4597 3.278495e-05 0.9999980 6 28
## 4599 4.373084e-05 0.9999972 6 29
## 5060 4.633864e-05 0.9999969 6 31
## 425 4.748952e-05 0.9999978 5 19
## FDR
## 1268 0.01258083
## 56 0.01258083
## 136 0.01335335
## 2958 0.01434748
## 3608 0.01448775
## 2462 0.02388150
## 4597 0.02388150
## 4599 0.02421491
## 5060 0.02421491
## 425 0.02421491
##
## [1] "set_38"
## [1] "ORMDL2" "TRAV21" "NAP1L1P3" "RP3-340B19.5"
## [5] "GS1-124K5.2" "EEF1A1P14" "RP11-254B13.4" "RPSAP4"
## [9] "MTRNR2L3" "HSPA8P5" "HNRNPA1P50" "ANP32AP1"
## [13] "AL161784.1" "CPQ" "FOXP1" "RCAN3"
## [17] "BTG1" "TC2N" "GPR183" "SATB1"
## [21] "POU6F1" "ACTBP12" "CHRM3-AS2" "CTD-2017D11.1"
## [25] "RP1-313I6.12" "RP11-434H6.7"
## $immune
## category over_represented_pvalue
## 1580 gse20727 h2o2 vs ros inhibitor treated dc up 1.940795e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 1580 1 5 19 0.0009896112
##
## [1] "set_39"
## [1] "NDUFAF7" "ACADVL" "MTIF2" "MRPS33" "NDUFAF5" "CDK5RAP1"
## [7] "EARS2" "MTFMT" "SARS2" "GTPBP10" "THG1L" "ATPAF1"
## [13] "C6orf203" "MTO1" "MRRF" "GLUD1" "MALSU1" "MRPL55"
## [19] "NDUFS4" "METTL17" "MRPL48" "ZNF782" "MRPL23" "MRPL33"
## [25] "CCDC109B"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 495 mitochondrial translation 0.000000e+00 1
## 986 translation 1.281153e-07 1
## numDEInCat numInCat FDR
## 495 8 9 0.000000e+00
## 986 10 46 6.546692e-05
##
## $go_bp
## category over_represented_pvalue
## 1301 mitochondrial gene expression 0.000000e+00
## 1311 mitochondrial translation 0.000000e+00
## 1307 mitochondrial rna metabolic process 3.346653e-07
## 3989 trna metabolic process 2.827013e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1301 1.0000000 12 16 0.0000000000
## 1311 1.0000000 10 13 0.0000000000
## 1307 1.0000000 5 7 0.0004559257
## 3989 0.9999984 6 23 0.0288850024
##
## [1] "set_40"
## [1] "BCL3" "GTSE1" "RGS1" "CCDC77" "SMUG1"
## [6] "IFI6" "GLUL" "BRIP1" "IRF4" "PHAX"
## [11] "HOPX" "CXCR6" "PDDC1" "EFCAB7" "RNU2-2P"
## [16] "MIR155HG" "AC011747.4" "DGKA" "SKIL" "RASGEF1B"
## [21] "NPIPB3" "PER1" "NPIPB4" "KLRK1" "NPIPB5"
## [26] "MTATP6P1"
## $immune
## category over_represented_pvalue
## 1806 gse22103 unstim vs lps stim neutrophil up 2.107416e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 1806 1 5 12 0.01074572
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8958527 478.5 17165476 916.8 NA 17165476 916.8
## Vcells 19141219 146.1 57216267 436.6 65536 78485130 598.8
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] goseq_1.50.0
## [12] geneLenDataBase_1.34.0
## [13] BiasedUrn_2.0.10
## [14] fgsea_1.24.0
## [15] biomaRt_2.54.1
## [16] limma_3.54.2
## [17] tidyr_1.3.0
## [18] ggpubr_0.6.0
## [19] ggplot2_3.4.2
## [20] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 tools_4.2.3
## [9] backports_1.4.1 bslib_0.4.2
## [11] utf8_1.2.3 R6_2.5.1
## [13] mgcv_1.8-42 DBI_1.1.3
## [15] colorspace_2.1-0 withr_2.5.0
## [17] tidyselect_1.2.0 prettyunits_1.1.1
## [19] bit_4.0.5 curl_5.0.1
## [21] compiler_4.2.3 cli_3.6.1
## [23] xml2_1.3.4 DelayedArray_0.24.0
## [25] rtracklayer_1.58.0 sass_0.4.5
## [27] scales_1.2.1 rappdirs_0.3.3
## [29] Rsamtools_2.14.0 stringr_1.5.0
## [31] digest_0.6.31 rmarkdown_2.21
## [33] XVector_0.38.0 pkgconfig_2.0.3
## [35] htmltools_0.5.5 MatrixGenerics_1.10.0
## [37] dbplyr_2.3.2 fastmap_1.1.1
## [39] rlang_1.1.0 rstudioapi_0.14
## [41] RSQLite_2.3.1 BiocIO_1.8.0
## [43] jquerylib_0.1.4 generics_0.1.3
## [45] jsonlite_1.8.4 BiocParallel_1.32.6
## [47] dplyr_1.1.2 car_3.1-2
## [49] RCurl_1.98-1.12 magrittr_2.0.3
## [51] GO.db_3.16.0 GenomeInfoDbData_1.2.9
## [53] Matrix_1.6-4 Rcpp_1.0.10
## [55] munsell_0.5.0 fansi_1.0.4
## [57] abind_1.4-5 lifecycle_1.0.3
## [59] stringi_1.7.12 yaml_2.3.7
## [61] carData_3.0-5 SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0 BiocFileCache_2.6.1
## [65] grid_4.2.3 blob_1.2.4
## [67] parallel_4.2.3 crayon_1.5.2
## [69] lattice_0.20-45 splines_4.2.3
## [71] Biostrings_2.66.0 cowplot_1.1.1
## [73] hms_1.1.3 KEGGREST_1.38.0
## [75] knitr_1.44 pillar_1.9.0
## [77] rjson_0.2.21 ggsignif_0.6.4
## [79] codetools_0.2-19 fastmatch_1.1-3
## [81] XML_3.99-0.14 glue_1.6.2
## [83] evaluate_0.20 png_0.1-8
## [85] vctrs_0.6.2 gtable_0.3.3
## [87] purrr_1.0.1 cachem_1.0.7
## [89] xfun_0.39 broom_1.0.4
## [91] restfulr_0.0.15 rstatix_0.7.2
## [93] tibble_3.2.1 GenomicAlignments_1.34.1
## [95] memoise_2.0.1